Scoring methods for anti-pd therapy eligibility and compositions for performing same

ABSTRACT

Aspects of the present disclosure provide methods for determining the eligibility of a subject having a malignancy for treatment with an anti-PD therapeutic agent based on a Combined Positive Score (CPS) for a tumor tissue sample from the subject. Compositions and kits or performing the disclosed methods are also provided.

CROSS-REFERENCING

This application is a continuation application of U.S. patentapplication Ser. No. 16/804,395 filed Feb. 28, 2020, which is acontinuation of U.S. patent application Ser. No. 15/422,350, filed Feb.1, 2017 and issued as U.S. Pat. No. 10,613,092 which claims the benefitof priority to U.S. provisional application 62/317,179, filed Apr. 1,2016, all applications are incorporated herein by reference.

BACKGROUND

Programmed cell death 1 ligand 1 (PD-L1) expression is implicated inevasion of immune responses involved in many contexts, includingsuppression of anti-tumor immune activity. PD-L1 expression has beenshown in situ on a wide variety of solid tumors including breast, lung,colon, ovarian, melanoma, bladder, liver, salivary, stomach, gliomas,thyroid, thymic epithelial, and head and neck cancers (Brown J A et al.,2003. J. Immunol. 170:1257-66; Dong H et al. 2002. Nat. Med. 8:793-800;Hamanishi J, et al. 2007. Proc. Natl. Acad. Sci. USA 104:3360-65; StromeS E et al. 2003. Cancer Res. 63:6501-5; Inman B A et al. 2007. Cancer109:1499-505; Konishi Jet. al. 2004. Clin. Cancer Res. 10:5094-100;Nakanishi Jet. al. 2007. Cancer Immunol. Immunother. 56:1173-82; Nomi Tet al. 2007. Clin. Cancer Res. 13:2151-57; Thompson R H et al. 2004.Proc. Natl. Acad. Sci. USA 101:17174-79; Wu C, Zhu Y, Jiang J, Zhao J,Zhang X G, Xu N. 2006. Acta Histochem. 108:19-24). In addition, PD-1expression can be upregulated on tumor infiltrating lymphocytes (TILs),and this may also contribute to tumor immunosuppression (Blank C et al.2003. J. Immunol. 171:4574-81).

In ovarian cancer, PD-L1 expression is inversely correlated withintraepithelial, but not stromal, infiltrating CD8 T cells, suggestingthat PD-L1 inhibits the intratumor migration of CD8 T cells (Hamanishi Jet. al. 2007. Proc. Natl. Acad. Sci. USA 104:3360-65). Translation ofPD-L1 mRNA is enhanced by loss of PTEN and the ensuing activation ofAkt, a common event in tumorigenesis (Parsa A T et al. 2007. Nat. Med.13:84-88). Studies relating PD-L1 expression on tumors to diseaseoutcome show that PD-L1 expression strongly correlates with unfavorableprognosis in kidney, ovarian, bladder, breast, gastric, and pancreaticcancer (Hamanishi J et al. 2007. Proc. Natl. Acad. Sci. USA 104:3360-65;Inman B A et al. 2007. Cancer 109:1499-505; Konishi J et. al. 2004.Clin. Cancer Res. 10:5094-100; Nakanishi J et. al. 2007. Cancer Immunol.Immunother. 56:1173-82; Nomi T et al. 2007. Clin. Cancer Res.13:2151-57; Thompson R H et al. 2004. Proc. Natl. Acad. Sci. USA101:17174-79; Wu C, Zhu Y, Jiang J, Zhao J, Zhang X G, Xu N. 2006. ActaHistochem. 108:19-24). In addition, these studies suggest that higherlevels of PD-L1 expression on tumors may facilitate advancement of tumorstage and invasion into deeper tissue structures. Studies in animalmodels demonstrate that PD-L1 on tumors inhibits T cell activation andlysis of tumor cells and in some cases leads to increased tumor-specificT cell death (Dong H et al. 2002. Nat. Med. 8:793-800; Hirano F et al.2005. Cancer Res. 65:1089-96).

Non-malignant cells have also been implicated in playing important rolesin tumor maintenance and growth. For example, tumor-associated APCs canutilize the PD-1:PD-L pathway to control antitumor T cell responses(Curiel et al. 2003. Nat. Med. 9:562-67). In this study, PD-L1expression on a population of tumor-associated myeloid DCs was shown tobe up-regulated by tumor environmental factors.

Given the role PD-1/PD-L1 plays in tumor biology, therapeutic agentsthat target this molecule have been of significant interest. Indeed,anti-PD-1/PD-L1 therapy (or anti-PD therapy) has generated significantclinical benefits by inducing regression of advanced and metastatictumors and improving survival. Anti-PD therapy can have durable effects,tolerable toxicity, and is applicable to a broad spectrum of cancertypes, especially in solid tumors.

Examples of anti-PD therapeutics currently in use or in developmentinclude the following:

Nivolumab, Bristol-Myers Squibb (also known as Opdivo, MDX-1106,BMS-936558, and ONO-4538), was the first mAb targeting PD-1 to showsignificant clinical activity in unresectable or metastatic melanomas,non-small-cell lung carcinoma (NSCLC), and metastatic renal cellcarcinomas.

Pembrolizumab, Merck (also known as Keytruda, lambrolizumab, andMK-3475), is an Anti-PD-1 monoclonal antibody that has shown similarefficacy and safety compared with nivolumab in a phase I clinical trialin advanced melanoma (NCT01295827) and is now an FDA-approvedsecond-line drug for the treatment of melanoma. Pembrolizumab is alsoeffective in patients with advanced NSCLC and has shown promisingeffects in other solid tumors, including advanced gastric cancer,advanced bladder cancer, head and neck cancer, classical Hodgkin'slymphoma, and triple-negative breast cancer.

BMS-936559, Bristol-Myers Squibb (also known as MDX-1105) is a fullyhuman IgG4 anti-PD-L1 mAb that inhibits the binding of the PD-L1 ligandto both PD-1 and CD80 and has demonstrated therapeutic efficacy in aphase I clinical trial (NCT00729664).

MPDL3280A, Genentech/Roche, is an engineered anti-PD-L1 IgG1 mAb thatcan inhibit PD-L1 interactions with both PD-1 and B7-1. A study ofmetastatic urothelial bladder cancer (UBC) demonstrated that MPDL3280Ahas marked activity in controlling tumor growth. Moreover, owing to themild side effects, including a lack of renal toxicity, patients withUBC, who are often older and have a higher incidence of renalimpairment, are thought to tolerate MPDL3280A better than chemotherapy(NCT01375842). In an expansion phase I trial across multiple cancertypes, including NSCLC, melanoma, renal cell carcinoma, and othertumors, responses to MPDL3280A were observed in patients with tumorsexpressing high levels of PD-L1, especially when PD-L1 was expressed bytumor infiltrating lymphocytes TILs.

Pidilizumab (Medivation/CureTech), MEDI4736 (AstraZeneca), and Avelumab(MSB0010718C; Merck-Sorono) are additional PD-L1 targetingantibody-based therapeutic agents that show promise in the treatment ofmultiple human cancers.

In addition to developing anti-PD therapeutic agents, work in this areahas included performing more detailed analysis of not only the malignantcells in tumor biopsies, but also non-malignant cells to identifypatients who may respond to these therapies. For example, some publishedscoring methods for PD-L1 immunohistochemistry (IHC) staining are eithercapturing percentage of staining and or staining intensity on tumorcells or the PD-L1 staining and staining intensity on tumor-associatedimmune cells (Phillips et al. Appl Immunohistochem Mol Morphol. 2015Sep.; 23(8): 541-549) (Garon et al. N Engl J Med. 2015 May 21;372(21):2018-28. doi: 10.1056/NEJMoa1501824. Epub 2015 Apr. 19). Moreand more clinical trials indicated that in some tumor indications PD-L1staining on both tumor and tumor-associated immune cells is associatedwith clinical outcome (Rosenberg et al., The Lancet, DOI:dx.doi.org/10.1016/S0140-6736(16)00561-4; Allred D, et al. Mod Pathol.1998; 11:155-168).

While progress has been made in this area, it is clear that usingcurrent scoring methods to capture PD-L1 expression on tumor as well asnon-tumor cells (e.g., immune cells) is not practical from an assaydevelopment standpoint, as it can double the pathologist's workloadand/or lead to confusion with respect to having 2 different cutoffs (onefor tumor cells and one for non-tumor cells). There is thus still a needto improve tumor tissue scoring methods for identifying patients thatwill respond effectively to anti-PD therapy.

SUMMARY

Aspects of the present disclosure provide methods for determining theeligibility of a subject having a malignancy for treatment with ananti-PD therapeutic agent based on a Combined Positive Score (CPS) for atumor tissue sample from the subject. In certain embodiments, the methodincludes: determining the number of viable PD-L1 positive tumor cells,the number of viable PD-L1 negative tumor cells, and the number ofviable PD-L1 positive mononuclear inflammatory cells (MIC) in a tumortissue sample from a subject having a malignancy; and calculating acombined positive score (CPS) for the tumor tissue sample using theformula:

${CPS} = {\frac{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{positive}{MIC}}}{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{negative}{tumor}{cells}}} \times 100\%}$

wherein the subject is eligible for treatment with an anti-PDtherapeutic agent when the CPS is above a threshold. Compositions andkits for performing the methods are also provided.

BRIEF DESCRIPTION OF THE FIGURES

The patent or application file contains at least one drawing executed incolor. Copies of this patent or patent application publication withcolor drawing(s) will be provided by the U.S. Patent and TrademarkOffice upon request and payment of the necessary fee.

Certain aspects of the following detailed description are bestunderstood when read in conjunction with the accompanying drawings. Itis emphasized that, according to common practice, the various featuresof the drawings are not to scale. On the contrary, the dimensions of thevarious features are arbitrarily expanded or reduced for clarity.Included in the drawings are the following figures:

FIG. 1 provides an example of rules for evaluating control samples.

FIG. 2 provides images of positive (left panel) and negative (rightpanel) control cell staining.

FIG. 3 provides a cartoon of a tissue section with a small stainingarea.

FIG. 4 provides a cartoon of a tissue section with a heterogenous tumorarea.

FIG. 5 provides images of a stained tissue sections showing differentintensities of PD-L1 on tumor cells. Top left panel shows negativestaining; top right panel shows weak staining; bottom left panel showsmoderate staining; and bottom right panel shows strong staining. Arrowsindicate stained cells in the relevant panels.

FIG. 6 provides an image of a stained tissue section showing PD-L1positive inflammatory cells. Arrows indicate positively stained cells.

FIG. 7 provides an image of a stained tissue section showing cytoplasmicand membrane staining. Labeled arrows show complete staining, partialstaining, cytoplasmic staining, and membrane staining.

FIG. 8 provides an image of a stained tissue section showing anedge-staining artifact (example of artifact indicated by arrow).

FIG. 9 provides an image of a stained tissue section showing acytoplasmic blush artifact (example of artifact indicated by arrow).

FIG. 10 provides an image of a stained tissue section showing theartifact of staining of necrotic tissue (examples of artifact indicatedby arrows).

FIG. 11 provides an image of a stained tissue section showing an exampleof HNSCC with a CPS of 0%. Examples of negative MIC and tumor cells areindicted with arrows.

FIG. 12 provides an image of a stained tissue section showing Example ofHNSCC with a CPS of 1%. Examples of negative and positive MICs and tumorcells are indicated with arrows.

FIG. 13 provides an image of a stained tissue section showing Example ofHNSCC with a CPS of 55%. Examples of negative and positive MICs andtumor cells are indicated with arrows.

FIG. 14 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 0%. Examples of negative MIC and tumorcells are indicted with arrows.

FIG. 15 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 1%. Examples of negative and positiveMICs and negative tumor cells are indicted with arrows.

FIG. 16 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 10%. Examples of negative and positiveMICs and tumor cells are indicated with arrows.

FIG. 17 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 40%. Examples of negative and positiveMICs and tumor cells are indicated with arrows.

FIG. 18 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 100%. Example of positive tumor cell isindicated with an arrow.

DEFINITIONS

Unless defined otherwise herein, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this invention belongs. Although any methodsand materials similar or equivalent to those described herein can beused in the practice or testing of the present invention, the preferredmethods and materials are described.

All patents and publications, including all sequences disclosed withinsuch patents and publications, referred to herein are expresslyincorporated by reference.

Numeric ranges are inclusive of the numbers defining the range. Unlessotherwise indicated, nucleic acids are written left to right in 5′ to 3′orientation; amino acid sequences are written left to right in amino tocarboxy orientation, respectively.

The headings provided herein are not limitations of the various aspectsor embodiments of the invention. Accordingly, the terms definedimmediately below are more fully defined by reference to thespecification as a whole.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention belongs. Singleton, et al., DICTIONARYOF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2D ED., John Wiley and Sons, NewYork (1994), and Hale & Markham, THE HARPER COLLINS DICTIONARY OFBIOLOGY, Harper Perennial, N.Y. (1991) provide one of skill with thegeneral meaning of many of the terms used herein. Still, certain termsare defined below for the sake of clarity and ease of reference.

The term “PD-L1” refers to the Programmed cell death ligand 1 molecule.PD-L1 may refer to human PD-L1 or homologs in other organisms, dependingon the context in which it is used. Human PD-L1 is also known as CD274,B7-H, B7H1, B7-H1, B7 homolog 1, MGC142294, MGC142296, PDCD1L1,PDCD1LG1, PDCD1 ligand 1, PDL1, Programmed cell death 1 ligand 1 andProgrammed death ligand 1 and has Uniprot number Q9NZQ7 and NCBI gene IDnumber 29126. Human PD-L1 is a 290 amino acid type I transmembraneprotein encoded by the CD274 gene on human chromosome 9. Mouse PD-L1 hasNCBI GenBank ID number ADK70950.1.

A “diagnostic marker” is a specific biochemical in the body which has aparticular molecular feature that makes it useful for detecting adisease, measuring the progress of disease or the effects of treatment,or for measuring a process of interest.

The term “epitope” as used herein is defined as small chemical groups onthe antigen molecule that is bound to by an antibody. An antigen canhave one or more epitopes. In many cases, an epitope is roughly fiveamino acids or sugars in size. One skilled in the art understands thatgenerally the overall three-dimensional structure or the specific linearsequence of the molecule can be the main criterion of antigenicspecificity.

A “subject” of diagnosis or treatment is a plant or animal, including ahuman. Non-human animals subject to diagnosis or treatment include, forexample, livestock and pets.

As used herein, the term “tissue section” refers to a piece of tissuethat has been obtained from a subject and mounted on a planar surface,e.g., a microscope slide. The sample may be fixed and/or sectioned asdesired. A “tumor tissue sample” or “tumor tissue biopsy sample”includes cells derived from a tumor in a subject, e.g., a human subjecthaving a malignancy. Such tissue samples are sometimes referred tosimply as a “biopsy”.

A “cell suspension” is used to refer to any cellular sample in whichsingle cells or very small cell aggregates are suspended in a liquidmedium. Cell suspensions are used, e.g., in flow cytometry and othersingle-cell analysis methods. Cell suspensions can be obtained byprocessing a solid tissue sample from a subject, e.g., by treating thesample with enzymes, chemicals, and/or placing them under physicallydisruptive conditions that disaggregate the cells. Such methods areknown in the art.

As used herein, the term “formalin-fixed paraffin embedded (FFPE) tissuesection” refers to a piece of tissue, e.g., a biopsy that has beenobtained from a subject, fixed in formaldehyde (e.g., 3%-5% formaldehydein phosphate buffered saline) or Bouin solution, embedded in wax, cutinto thin sections, and then mounted on a planar surface, e.g., amicroscope slide.

As used herein, the term “resin embedded tissue section” refers to apiece of tissue, e.g. a biopsy that has been obtained from a subject,fixed, (e.g., in 3-5% glutaraldehyde in 0.1M phosphate buffer),dehydrated, infiltrated with epoxy or methacrylate resin, cured, cutinto thin sections, and then mounted on a planar surface, e.g., amicroscope slide.

As used herein, the term “cryosection” refers to a piece of tissue, e.g.a biopsy that has been obtained from a subject, snap frozen, embedded inoptimal cutting temperature embedding material, frozen, cut into thinsections and fixed (e.g. in methanol or paraformaldehyde) and mounted ona planar surface, e.g., a microscope slide.

The term “staining” includes binding a target (e.g., an antigen) in acellular sample with a target-specific binding agent (e.g., an antibodyor a nucleic acid) and then detecting the presence of thetarget-specific binding agent on the cells of the cellular sample usinga detectable label or chromogen. The detectable label can be directlyconjugated to the target-specific binding agent (e.g., a primaryantibody) or may be conjugated to a secondary reagent that bindsspecifically to an unlabeled target-specific reagent (e.g., a secondaryantibody). In some cases, the target-specific reagent is itselfdetectable, and thus no additional attached label is needed.

By “fluorophore” or “fluorescent label” is meant any label that absorbslight at a first wavelength (or range of wavelengths) and emits light ata second, different wavelength (or range of wavelengths). In general,the emitted light from a fluorescent labels has a longer wavelength, andtherefore lower energy, than the absorbed wavelength. Examples offluorescent labels include, but are not limited to, phycobiliproteins(e.g., phycoerythrin (PE), phycocyanin (PC), allophycocyanin (APC)),rhodamine, fluorescein, alexa fluor, cascade blue, tetramethylrhodamine,Texas red, and the like, as well as those listed in greater detailbelow.

A “chromogen” or “chromogenic compound” and the like is a substance thatcan be converted into a colored compound under specific conditions,e.g., when acted upon by an enzyme or under specific chemical/reactionconditions. Examples of enzyme-substrate combinations include: (i)Horseradish peroxidase (HRP) with hydrogen peroxidase as a substrate,where the hydrogen peroxidase oxidizes a dye precursor [e.g.,orthophenylene diamine (OPD) or 3,3′,5,5′-tetramethyl benzidinehydrochloride (TMB)]; (ii) alkaline phosphatase (AP) withpara-Nitrophenyl phosphate as chromogenic substrate; and (iii)β-D-galactosidase (β-D-Gal) with a chromogenic substrate (e.g.,p-nitrophenyl-β-D-galactosidase) or fluorogenic substrate (e.g.,4-methylumbelliferyl-β-D-galactosidase). Numerous other enzyme-substratecombinations are available to those skilled in the art. For a generalreview of these, see U.S. Pat. Nos. 4,275,149 and 4,318,980.

As used herein, the term “target-specific binding agent” means any agentthat specifically binds to a target or analyte of interest, e.g., atarget of interest that is present in a tissue section as describedherein (e.g., a polypeptide or polynucleotide). Examples oftarget-specific binding agents include antibodies, receptors, andligands, or target-binding fragments thereof, polynucleotide probes, andthe like.

As used herein, the term “multiplexing” refers to using more than onelabel, stain, and/or chromogen for the simultaneous or sequentialdetection and measurement of a target in a sample, e.g., a tissuesection.

As used herein, the terms “antibody” and “immunoglobulin” are usedinterchangeably and are well understood by those in the field. Thoseterms refer to a protein consisting of one or more polypeptides thatspecifically binds an antigen. One form of antibody constitutes thebasic structural unit of an antibody. This form is a tetramer andconsists of two identical pairs of antibody chains, each pair having onelight and one heavy chain. In each pair, the light and heavy chainvariable regions are together responsible for binding to an antigen, andthe constant regions are responsible for the antibody effectorfunctions. These terms also include fragments of antibodies which retainspecific binding to antigen or target, including, but not limited to,Fab, Fv, scFv, and Fd fragments, chimeric antibodies, humanizedantibodies, single-chain antibodies, bi-specific hybrid antibodies, andfusion proteins comprising an antigen-binding portion of an antibody anda non-antibody protein. See, e.g., Hood et al., “Immunology”, Benjamin,N.Y., 2nd ed. (1984); Hunkapiller and Hood, Nature, 323, 15-16 (1986);Lanzavecchia et al., Eur. J. Immunol. 17, 105-111 (1987); Huston et al.,Proc. Natl. Acad. Sci. U.S.A., 85, 5879-5883 (1988); and Bird et al.,Science, 242, 423-426 (1988) which are hereby incorporated by referenceherein in their entirety.

As used herein, the terms “primary antibody” and “secondary antibody”refer to different antibodies, where a primary antibody is a polyclonalor monoclonal antibody from one species (rabbit, mouse, goat, donkey,etc.) that specifically recognizes an antigen (e.g., a biomarker) in asample (e.g., a human tissue sample) under study, and a secondaryantibody is an antibody (usually polyclonal) from a different speciesthat specifically recognizes the primary antibody, e.g., in its Fcregion.

Sometimes, the label may be indirectly conjugated with the antibody. Theskilled artisan will be aware of various techniques for achieving this.For example, the antibody can be conjugated with biotin and any of thefour broad categories of labels mentioned above can be conjugated withavidin, or vice versa. Biotin binds selectively to avidin and thus, thelabel can be conjugated with the antibody in this indirect manner.Alternatively, to achieve indirect conjugation of the label with theantibody, the antibody may be conjugated with a small hapten and one ofthe different types of labels mentioned above is conjugated with ananti-hapten antibody. Thus, indirect conjugation of the label with theantibody can be achieved. In some embodiments of the invention one ormore secondary antibody molecules may be conjugated with alabel-conjugated polymer backbone. Thus, amplification of the signal maybe achieved.

Indirectly and directly labeled secondary antibodies are alsocommercially available. For example, one example of commerciallyavailable label-conjugated polymer backbone carrying secondary antibodymolecules reagent is EnVision™ reagent (DAKO). A secondary antibodycarrying a label aimed for a particular type of detection may beobtained from numerous manufacturers.

The term “specific binding” refers to the ability of a binding agent topreferentially bind to a particular analyte that is present in ahomogeneous mixture of different analytes. In certain embodiments, aspecific binding interaction will discriminate between desirable andundesirable analytes in a sample, in some embodiments more than about 10to 100-fold or more (e.g., more than about 1000- or 10,000-fold).

In certain embodiments, the affinity between a binding agent and analytewhen they are specifically bound in a capture agent/analyte complex ischaracterized by a KD (dissociation constant) of less than 10-6 M, lessthan 10-7 M, less than 10-8 M, less than 10-9 M, less than 10-10 M, lessthan 10-11 M, or less than about 10-12 M or less.

A “plurality” contains at least 2 members. In certain cases, a pluralitymay have at least 10, at least 100, at least 1000, at least 10,000, atleast 100,000, at least 106, at least 107, at least 108 or at least 109or more members.

Other definitions of terms may appear throughout the specification.

DETAILED DESCRIPTION

In order to further illustrate the present invention, the followingspecific examples are given with the understanding that they are beingoffered to illustrate the present invention and should not be construedin any way as limiting its scope.

As summarized above, aspects of the present disclosure include methodsfor determining the eligibility of a subject having a malignancy fortreatment with an anti-PD therapeutic agent. In certain embodiments, themethod includes determining a Combined Positive Score (CPS) for PD-L1expression in a tumor sample from a subject. We have found that use ofthe disclosed CPS dramatically decreases the work load for pathologistsin the clinic, is easier to apply, produces higher inter-observer andintra-observer concordances, and identifies subjects eligible foranti-PD therapy who would otherwise be missed using other scoringmethods focusing solely on biomarker expression on tumor cells.

The CPS is calculated by: determining the number of viable PD-L1positive tumor cells, the number of viable PD-L1 negative tumor cells,and the number of viable PD-L1 positive mononuclear inflammatory cells(MIC) in a tumor tissue sample from a subject having a malignancy; andcalculating the CPS using the following formula:

${CPS} = {\frac{{\#{PD} - L1{positive}{tumor}{cells}} + {\#{PD} - L1{positive}{MIC}}}{{\#{of}{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{negative}{tumor}{cells}}} \times 100\%}$

Although the score can be calculated as greater than 100%, the maximumCPS is defined as 100%. The specimen is considered PD-L1 positive (andthus the subject eligible for treatment with anti-PD therapy) if CPS isabove a threshold level. Thresholds can be determined by a ROC curve forbest responder/cut off (threshold) correlation. Threshold (or cutoffs/cut points) can thus be any applicable CPS value, including but notlimited to: 1%; 5%; 10%; 20% 30%; 40%; 50%; 60%, etc., and is specificto the drug used. In some embodiments, the threshold is set at 1%. Insuch embodiments, the specimen is considered PD-L1 positive if CPS ≥1%(i.e., equal to or above the threshold value). PD-L1 positive cells areviable cells (tumor or mononuclear inflammatory cells) that exhibitmembrane staining at any intensity over background.

PD-L1 expression of the specimen is determined by the Combined PositiveScore (CPS). In certain embodiments, the tissue sample (or specimen)must contain a minimum number of viable cells for evaluation, e.g., atleast 50 viable tumor cells, at least 100 viable tumor cells, at least150 viable tumor cells, at least 250 viable tumor cells, etc. By viablecells is meant that the cells were viable at the time they wereharvested from the subject, and not necessarily viable at the time ofstaining. For example, where tumor biopsy sample slides are analyzed,the cells are considered viable cells if they are deemed, uponobservation and analysis, to have been viable at the time the tumorbiopsy was harvested. If the specimen contains the minimum number ofviable cells, the specimen is evaluable using the CPS method, e.g., bycalculating an eligibility score.

Detecting PD-L1 positive cells in a tumor sample can be done in anyconvenient manner.

In certain embodiments, the CPS is calculated from a stained tumortissue biopsy section (e.g., on a slide) or serial tumor tissue biopsysections by immunohistochemistry (IHC) staining, in-situ hybridization(ISH; e.g., fluorescence-in-situ-hybridization, or FISH), histologicalstain, and combinations thereof. In certain embodiments, a tumor tissuebiopsy section is analyzed by IHC to calculate the CPS. In certain ofthese embodiments, the percentage of viable PD-L1 positive and negativetumor cells and PD-L1 positive mononuclear inflammatory cells (MIC) isdetermined within the tumor nests and the adjacent supporting stroma. Insuch embodiments, cells are positive for PD-L1 staining if they displaypartial or complete membrane staining relative to all viable tumor cellspresent in the sample.

It is noted here that patients with advanced-stage disease of certaintumor types (e.g., non small cell lung carcinoma (NSCLC)) are oftendiagnosed on a small biopsy or cytology specimen obtained through aminimally invasive procedure. These small biopsy or cytology specimensare often the only samples available for testing. The methods describedherein are especially attractive for cytology specimens such as these,i.e., those in which the context of the tissue architecture is lost andit is very challenging to distinguish tumor from immune cells. Suchsamples include fine needle aspirates (where a thin needle is insertedinto an area of abnormal-appearing tissue) or body fluid for sampling ofcells. It can be the case that using CPS or a variation thereof is theonly reliable method to analyze these specimens.

In other embodiments, the CPS is calculated from a tumor tissue samplethat is not a fixed section on a slide. For example, in certainembodiments, the CPS is calculated using flow cytometric analysis of acell suspension from the tumor tissue sample. In these embodiments, thetumor tissue cell suspension can be stained with a detectable PD-L1binding agent (e.g., a fluorescently labeled antibody) and analyzed on aflow cytometer for counting the number of tumor cells and MIC cellsexpressing PD-L1. Tumor cells and MIC in the sample can be distinguishedusing any convenient flow cytometric parameter, e.g., forward scatter(FS), side scatter (SS), or by the expression of one or more additionalmakers using corresponding detectable binding agents for the one or moreadditional markers, e.g., markers specific or MIC or tumor cells. Inother embodiments, the cells in the tumor tissue sample can be analyzedon a cell-by-cell basis for mRNA expression of PD-L1 and any otherdesired target, e.g., using single-cell nucleic acid sequencing methodsfor gene expression profiling (e.g., next generation sequencingmethods).

As noted above, certain embodiments of the disclosed methods includestaining the tumor tissue biopsy section for at least one (or multiple)additional target(s) or with a stain. Where multiple targets areassessed, e.g., a cell type-specific marker or a second tumor cellmarker, the staining process may be done in a multiplex fashion, i.e.,all desired markers are assessed on the same tissue samplesimultaneously (e.g., using detectably distinguishable target-specificbinding agents). In other embodiments, the multiple targets are detectedon separate tissue samples, e.g., serial tissue sections derived fromthe same tumor biopsy from the subject. In embodiments where anadditional stain is employed, the stain can be a histological stain,including but not limited to hematoxylin and eosin (H&E stain), which isthe most commonly used light microscopy stain in histology andhistopathology. Hematoxylin, a basic dye, stains nuclei blue due to anaffinity to nucleic acids in the cell nucleus; eosin, an acidic dye,stains the cytoplasm pink. Another commonly performed histochemicaltechnique is the Perls Prussian blue reaction, used to demonstrate irondeposits in diseases like hemochromatosis. In some embodiments, thetissue sample is stained with a viability stain or dye to enhance theidentification of viable cells. For example, a tissue sample analyzed byflow cytometry can be contacted with a viability dye prior to analysis,e.g., propidium iodide. Any convenient viability stain may be employed,with many examples known in the art. Further, there are many otherstaining techniques known in to those of skill in the art that can beused to selectively stain cells and cellular components that find use inthe present disclosure, and as such no limitation in this regard isintended.

The staining of a target (e.g., PD-L1) in cells from a tumor tissuebiopsy is generally done by contacting the cells with one or moredetectable target-specific binding agents under suitable conditions toallow for binding of the target-specific binding agent to its desiredtarget (while minimizing non-target binding). As noted above, the term“target-specific binding agent” means any agent that specifically bindsto a target or analyte of interest, e.g., a target of interest that ispresent in a tissue section as described herein (e.g., a polypeptide orpolynucleotide). In some embodiments, the target-specific binding agentis an antibody (or target-binding fragments thereof), e.g., as used inIHC and flow cytometry. Staining may be performed with primary andsecondary antibodies or without using secondary antibodies (e.g., wherethe primary antibody is detectably labeled). Non limiting examples ofanti-PD-L1 antibodies include, but are not limited to, clone 22C3 (Merck& Co.), clone 28-8 (Bristol-Myers Squibb), and clones SP263 or SP142(Spring Biosciences). In certain other embodiments, the target-specificbinding agent is a nucleic acid or nucleic acid binding agent, e.g., asemployed in in situ hybridization (ISH) reactions. For example, thetarget binding reagent can be a DNA, RNA, DNA/RNA hybrid molecule,peptide nucleic acid (PNA), and the like. No limitation in the metes andbounds of a target-specific binding agent that finds use in the subjectdisclosure is intended.

The target-specific binding agent (or any secondary reagent used todetect the target-specific binding agent) may be attached to anysuitable detectable label (or chromogen) or enzyme capable of producinga detectable label. Thus, in certain embodiments, the first or secondlabel is produced by an enzymatic reaction, e.g., by the activity ofhorseradish peroxidase, alkaline phosphatase, and the like. Anyconvenient enzymatic label/chromogen deposition system can be employed(e.g., as used in standard IHC methods), and as such, no limitation inthis regard is intended. In some embodiments, the detectable label is afluorescent tag.

In some embodiments, the staining reagents used may include atarget-specific antibody (e.g., a PD-L1 specific antibody). Where anadditional target is to be detected, the staining reagents used mayinclude one or more additional antibodies that each bind to a differentantigen. For example, a set of antibodies may include a first antibodythat binds to a first antigen (e.g., PD-L1), a second antibody thatbinds to a second antigen, a third antibody that binds to a thirdantigen and, optionally a fourth antibody that binds to a fourth antigenand/or further antibodies that bind to further antigens. In someembodiments, the antibody/antibodies used are primary antibodies thatare detected by use of a secondary antibody (or other reagent). Thestaining steps thus may be done by incubating the cells of the tissuesample, e.g., a tissue section or cell suspension, with the primaryantibody/antibodies and then, after the primary antibody has bound tothe desired target in/on the cells, incubating the cells with thelabeled secondary antibody/antibodies (e.g., as is done in standard IHCprotocols). In some multiplex embodiments, each of the primaryantibodies for each different target is from a different species (e.g.,goat, rabbit, mouse, camel, chicken, donkey, etc.) and the correspondingsecondary antibodies specific for each different primary antibody aredistinguishably labeled from each other.

In some multiplex embodiments, the first and second (and subsequent)targets being detected are different from each other, e.g., aredifferent proteins or polynucleotides (e.g., different genes). However,in some multiplex embodiments, there may be some overlap. For example,in certain cases, a first target-specific binding agent may bind to thesame target as a second target-specific binding agent but at a differentepitope or site.

As noted above, the tissue sample (e.g., tissue section or cellsuspension) can be assessed for targets other than PD-L1. In certainembodiments, the additional target is one that identifies tumor cells.Examples include, but are not limited to: cytokeratin markers includingpan-CK cocktails, (e.g., AE1/AE3, CAM5.2/AE1) for adenocarcenomas andCK903 (34(3E12) for squamous cell carcinomas. In certain embodiments,the additional target is one that identifies MIC. Examples include, butare not limited to: CD3, CD5, CD4, CD7, CD8, CD20, and other markers ofMIC.

In certain embodiments, the sample being analyzed is a tissue section,e.g., a formalin fixed and paraffin embedded (FFPE) tissue section. Inalternative embodiments, the tissue section has been fixed in adifferent way, including tissue sections that have been fixed in, e.g.,acrolein, glyoxal, smium tetroxide, arbodiimide, mercuric chloride, zincsalts, picric acid, potassium dichromate, ethanol, methanol, acetone,and/or acetic acid.

In embodiments in which a tissue section is analyzed by microscopy, themethod further comprises comparing the relative location of the detectedfirst (or any subsequent) label on the tissue section(s). This can bedone, for example, by overlaying multiple images of the slide or seriesof slides that were collected during the analysis (e.g., for differentlabels). For example, one or more images collected for the labels of afirst tissue section (or first label) can be overlaid onto one or moreimages collected for a second adjacent tissue section (or second,distinguishable label).

In certain embodiments, the images may be overlaid and analyzed toidentify the boundaries of individual cells or regions in the tissuesection, and/or subcellular features in individual cells, in the image.Computer-implemented methods for segmenting images of cells and tissuesare known in the art and range from relatively simple thresholdingtechniques (see, e.g., Korde et al. Anal Quant Cytol Histol. 2009 31:83-89 and Tuominen et al. Breast Cancer Res. 2010 12: R56), to moresophisticated methods, such as, for instance, adaptive attention windowsdefined by the maximum cell size (Ko et al. J Digit Imaging. 2009 22:259-274) or gradient flow tracking (Li, et al. J Microsc. 2008 231:47-58). Some suitable image segmentation methods may be reviewed in Koet al. (J Digit Imaging. 2009 22: 259-74) and Ong et al. (Comput BiolMed. 1996 26:269-79). Next the data that corresponds to each of theindividual parameters that have been defined by the segmenting areintegrated to provide, for each cell, values that indicate which markersare associated with the cell. In certain cases, a cell may be identifiedas being malignant, non-malignant, infiltrating non-malignant, etc., asa result of this analysis. This data may allow one to potentially typethe cells in the sample. As such, this method may comprise displaying animage of the sample, in which the cells are color-coded by their type.

In certain embodiments, the tissue section may be a section of a tissuebiopsy obtained from a patient, e.g., a patient having a malignancy.Biopsies of interest include both tumor and non-neoplastic biopsies ofskin (melanomas, carcinomas, etc.), soft tissue, bone, breast, colon,liver, kidney, adrenal, gastrointestinal, pancreatic, gall bladder,salivary gland, cervical, ovary, uterus, testis, prostate, lung, thymus,thyroid, parathyroid, pituitary (adenomas, etc.), brain, spinal cord,ocular, nerve, and skeletal muscle, etc. In certain embodiments, thesubject from which the biopsy is obtained has a malignancy is selectedfrom: gastric cancer, esophageal carcinomas, head and neck cancer (e.g.,head and neck squamous cell carcinoma, or HNSCC), renal cell carcinoma,urothelial/bladder carcinoma, ovarian carcinoma, myeloma, melanoma, lungcancer, classical Hodgkin's lymphoma, and breast cancer (e.g., triplenegative breast cancer, hormone receptor positive (ER and/or PR) andHer2 positive breast cancer), small cell lung cancer, salivary glandcarcinoma, vulvar carcinoma, thyroid carcinoma, anal canal carcinoma,biliary carcinoma, mesothelioma, cervical carcinoma, and neuroendocrinecarcinoma.

In some embodiments, the method may involve obtaining one or more imageas described above (e.g., an electronic form of which may have beenforwarded from a remote location) and may be analyzed by a doctor orother medical professional to calculate the CPS. In other embodiments,the tissue sections are assessed in real time, i.e., not from a storedimage of the slide (or other form of stored data). In some embodiments,a slide or image of the slide, as described above, is assessed and a CPSis calculated in an automated fashion in silico, e.g., without theslide(s) or image(s) of the slide being assessed by a human. In suchembodiments, the slide(s)/image(s) are analyzed by a computer that hasbeen programmed to analyze the staining pattern and identify the PD-L1positive and negative tumor cells as well as the PD-L1 positive MICs. Inother embodiments, the image of the slide or slides is annotated by aslide imaging device such that cells of each different cell type (e.g.,PD-L1 positive tumor, PD-L1 negative tumor, and PD-L1 positive MIC) arereadily identifiable by a user, e.g., by color coding of the cells orregions in the image.

In any embodiment, data can be forwarded to a “remote location,” where“remote location” means a location other than the location at which theimage is examined. For example, a remote location could be anotherlocation (e.g., office, lab, etc.) in the same city, another location ina different city, another location in a different state, anotherlocation in a different country, etc. As such, when one item isindicated as being “remote” from another, what is meant is that the twoitems can be in the same room but be separated, or at least in differentrooms or different buildings, and can be at least one mile, ten miles,or at least one hundred miles apart. “Communicating” informationreferences transmitting the data representing that information aselectrical signals over a suitable communication channel (e.g., aprivate or public network). “Forwarding” an item refers to any means ofgetting that item from one location to the next, whether by physicallytransporting that item or otherwise (where that is possible) andincludes, at least in the case of data, physically transporting a mediumcarrying the data or communicating the data. Examples of communicatingmedia include radio or infra-red transmission channels as well as anetwork connection to another computer or networked device, and theinternet or include email transmissions and information recorded onwebsites and the like. In certain embodiments, the image may be analyzedby an MD or other qualified medical professional, and a report based onthe results of the analysis of the image may be forwarded to the patientfrom which the sample was obtained.

Specific Embodiments

The specific embodiments below are intended for illustration purposesonly and are not intended to be limiting.

The purpose of these embodiments is to provide guidelines for evaluatingPD-L1 expression on formalin-fixed, paraffin-embedded (FFPE) tumortissue section with Dako's PD-L1 IHC 22C3 pharmDx kit (SK006). Thisimmunohistochemical (IHC) assay is performed using the Dako AutostainerLink 48 automated staining system.

The embodiments below are described with respect to the use of the PD-L1IHC 22C3 pharmDx kit, which is a qualitative immunohistochemical assayusing Monoclonal Mouse Anti-PD-L1, Clone 22C3. This kit is intended foruse in the detection of PD-L1 protein in formalin-fixed,paraffin-embedded (FFPE) tumor tissue using EnVision FLEX visualizationsystem on Autostainer Link 48. Here, PD-L1 protein expression is used todetermine a Combined Positive Score (CPS; as describe above). In theseembodiments, the specimen is considered PD-L1 positive if the CPS ≥1%,where PD-L1 positivity is defined as a viable cell exhibiting membranestaining with the 22C3 antibody at any intensity (as compared topositive and negative controls, as described below).

PD-L1 IHC 22C3 pharmDx is indicated as an aid in identifying patientshaving a malignancy for treatment with KEYTRUDA® (pembrolizumab) (e.g.,patients with gastric carcinoma or HNSCC).

Definitions

Word/ Definition of Acronym Word/Word(s) for Acronym CPS CombinedPositive Score H&E Hemotaxylin and eosin MCF-7 PD-L1-negative controlcell line MIC Mononuclear inflammatory cells NCI-H226 PD-L1-positivecontrol cell line NCR Negative Control Reagent PD-L1 Programmed DeathLigand 1Clinical Interpretation Guidelines for PD-L1 IHC 22C3 pharmDx inTumorTissue Specimen Criteria

A hemotaxylin and eosin (H&E) stained section is recommended for theevaluation of an acceptable tumor tissue sample. PD-L1 IHC 22C3 pharmDxand the H&E staining is performed on serial sections from the sameparaffin block of the specimen to confirm:

1. The histological diagnosis of the cancer/malignancy.

2. The specimen contains a minimum of 100 viable tumor cells todetermine the percentage of positive cells. For patient specimens withless than 100 viable tumor cells, tissue from a deeper level of theblock, or potentially another block, could present sufficient number ofviable tumor cells for PD-L1 IHC 22C3 pharmDx testing.

3. The specimen has been properly fixed and prepared for IHC analysis.Well-preserved and well-stained areas of the specimen are used to make adetermination of the percentage of cells present (e.g., PD-L1 positivetumor cells).

Evaluating Controls

Deviations in the recommended procedures for tissue fixation, processingand embedding in the user's laboratory may produce significantvariability in results. Therefore, the following controls can beincluded in each staining run.

Quality Control Summary Control Type Reagents Used in Testing Purpose ofTesting Control Slide supplied by Dako Primary Antibody, Controlsstaining procedure *Negative Control Reagent only & Detection SystemPositive Control: Tissue or cells Primary Antibody, Negative Controlsall steps of the containing target antigen to be Control Reagent &analysis. Validates reagents and detected. The ideal control isDetection System procedures used for PD-L1 weakly positive stainingtissue, staining. which may be more sensitive in detecting reagentdegradation. Negative Control: Tissues or Primary Antibody, NegativeDetection of unintended cells expected to be negative Control Reagent &antibody cross-reactivity to (could be located in patient DetectionSystem cells/cellular components. tissue or positive control tissue).Patient tissue slide Negative Control Reagent & Detection ofnon-specific same Detection System as background staining. used with thePrimary Antibody *From the same species as the primary antibody, but notdirected against the same target antigen. To detect non-specificantibody binding, e.g. binding of Fc portion of antibody by the tissue.

All control tissues must meet acceptance criteria to proceed withevaluation of PD-L1 staining on gastric carcinoma tissues. (See FIG. 1for an example of the Rules to follow when evaluating controls.)

PD-L1 IHC 22C3 pharmDx Control Cell Line Slide

Examine the PD-L1 IHC 22C3 pharmDx control cell line slide to determinethat reagents are functioning properly. Each slide contains sections ofcell pellets with positive and negative PD-L1 expression. Assess thepercentage of positive cells and the staining intensity. If any stainingof the control cell line slide is not satisfactory, all results with thespecimens should be considered invalid. Control cell line slide is notused as an aid in interpretation of patient results.

Evaluate the overall staining intensity using the following guide:

0 Negative 1+ Weak Intensity 2+ Moderate Intensity 3+ Strong Intensity

FIG. 2 shows representative PD-L1 positive (left panel) and negative(right panel) control cell line staining. The PD-L1 positive cell lineNCI-H226 and the negative control cell line is MCF-7. As seen in thisfigure, at least 70% of the PD-L1 positive control cells contain cellmembrane staining of at least 2+ average staining intensity and anynon-specific staining is <1+ staining intensity. For the PD-L1 negativecell pellet, the majority of cells demonstrate no staining. (Thepresence of 10 or fewer cells with distinct cell membrane staining inthe negative control cell sample is generally acceptable). Anynon-specific staining is <1+ staining intensity.

User-Provided Control Tissue Slides

A user-provided positive control tissue slide is examined after thecontrol cell line slides described above. This slide verifies that thefixation method and epitope retrieval process are effective. The idealpositive control tissue provides a complete dynamic representation ofweak to moderate cell membrane staining of tumor cells and/or cellmembrane/cytoplasmic staining of tumor-associated mononuclearinflammatory cells (MICs). Use intact cells for interpretation ofstaining results because necrotic or degenerated cells often stainnon-specifically. Non-specific staining should be ≤1+.

A user-provided negative control tissue slide is also examined to verifythe specificity of the labeling of the target antigen by the primaryantibody. The ideal negative control tissue demonstrates no staining ontumor cells and MICs. The absence of specific staining in the negativecontrol tissue slide confirms the lack of kit cross-reactivity tocells/cellular components. The variety of different cell types presentin most tissue sections offers internal negative control sites; thisshould be verified by the user.

If staining of positive and/or negative control tissues are notsatisfactory, the results with the patient specimen should be consideredinvalid.

In addition, patient specimens are stained with a Negative ControlReagent (NCR) from the PD-L1 IHC 22C3 pharmDx kit. Specimens stainedwith the NCR should have 0 specific staining and ≤1+ non-specificstaining. Staining occurring in the cytoplasm of tumor cells of thespecimen treated with the NCR should be considered non-specificstaining.

Example of Scoring Guidelines

For evaluation of tissue section staining and scoring (e.g., using IHC),an objective of 10-20× magnification is used. Partial or complete cellmembrane staining of tumor cells that is perceived distinct fromcytoplasmic staining is considered positive, as is cellmembrane/cytoplasmic staining of MICs within the tumor nests and theadjacent supporting stroma. Adjacent MICs are defined as being withinthe same 20×field as the tumor. However, MICs that are NOT directlyassociated with the response against the tumor should be excluded. Forexample, in some cases, MICs are in the 20×field of view but can clearlybe directly linked to non-tumor related causes. Such MICs should beexcluded from scoring.

Refer to the table below for details in evaluating PD-L1 positivity.

Element Included in Scoring Excluded from Scoring Tumor cells Convincingpartial or complete Tumor cell cytoplasmic staining membrane staining(at any intensity) of viable carcinoma tumor cells Immune cells Membraneand/or cytoplasmic* Immune cells not infiltrating nor staining (at anyintensity) of adjacent to tumor mononuclear inflammatory Normal cellsadjacent to tumor cells (MIC) within tumor nests cells and adjacentsupporting Stromal cells (fibroblasts) stroma**, such as: Necrotic cellsand/or cellular Lymphocytes (lymphocyte debris that may stain PD-L1aggregates) positive Monocytes Plasma cells Macrophages NeutrophilsMorphology N/A Tissue damage/immune cells Patterns not responsive totumor (e.g., chronic inflammation) *Lymphocytes often presentindistinctive staining of membrane and cytoplasm due to a high nuclearto cytoplasmic ratio. Therefore, membrane and/or cytoplasmic staining inlymphocytes shall be included in the score. **Adjacent MICs are definedas being within the same 20× field as the tumor. However, MICs that areNOT directly associated with the response against the tumor should beexcluded.

Examples for Simple Calculations of CPS Example 1: Calculate CPS for aSpecimen Containing 100 Total Tumor Cells, 80 Positive Tumor Cells, and50 Positive Adjacent MICs

${CPS} = {\frac{{80{positive}{tumor}{cells}} + {50{positive}{MICs}}}{100{total}{tumor}{cells}} \times 100\%}$

In this case the CPS=100% (although the score is greater than 100%, themaximum CPS is defined as 100%). The specimen is thus scored as PD-L1Positive, and as such the subject is considered as eligible for anti-PDtherapy.

Example 2: Calculate CPS for a Specimen Containing 1000 Total TumorCells, 0 Positive Tumor Cells, 10 Positive Adjacent MICs

${CPS} = {\frac{{0{positive}{tumor}{cells}} + {10{positive}{MICs}}}{1000{total}{tumor}{cells}} \times 100\%}$

In this case the CPS=1%. The specimen is thus scored as PD-L1 Positive(the threshold is 1% in this example), and as such the subject isconsidered as eligible for anti-PD therapy.

Example 3: Calculate CPS for a Specimen Containing 1000 Total TumorCells, 5 Positive Tumor Cells, and 0 Positive Adjacent MICs

${CPS} = {\frac{{5{positive}{tumor}{cells}} + {0{positive}{MICs}}}{1000{total}{tumor}{cells}} \times 100\%}$

In this case the CPS=0.5%. The specimen is thus scored as PD-L1Negative, and as such the subject is not considered as eligible foranti-PD therapy.

Examples of More Complex Tissue Stains Example 1: Calculation ofCombined Positive Score in a Small Tumor Area with Staining

FIG. 3 shows a cartoon of a tissue section with a small staining area.At lower magnification (left), only about 10% of the tissue area isstained (90% of the tissue area is without staining). To calculate theCPS, the stained area is evaluated at a higher magnification (right) toestimate the number of PD-L1 positive and negative tumor cells andmononuclear inflammatory cells that are PD-L1 positive. In this area, 50out of 100 tumor cells are PD-L1 positive, and there are 34 mononuclearinflammatory cells that are PD-L1 positive. The CPS score of the stainedarea is thus:

${\frac{{50{positive}{tumor}{cells}} + {34{positive}{MICs}}}{100{tumor}{cells}} \times 100} = {84\%}$

Because only 10% of the sample was stained, the CPS score is adjusted bymultiplying the CPS of the stained area with the percentage of thetissue that was stained (in this case, 10%). The CPS score for theentire tissue sample is thus 10%×84%=8.4%. This specimen is thus abovethe threshold of 1% and is considered PD-L1 positive (and thus thesubject is eligible for anti-PD therapy).

Example 2: Calculation of Combined Positive Score in a HeterogeneousTumor Area

FIG. 4 shows a cartoon of a tissue section with a heterogenous tumorarea. At lower magnifications (upper left), the tissue sample isvisually divided into sections. A CPS for each section is determined byobserving them at higher magnification (lower right). CPS for each ofthe four respective sections is as follows (clockwise from top left:81%, 29%, 100%, and 53%. To get an overall CPS, these four scores areaveraged, giving an overall CPS of 65%. This specimen is thus above thethreshold of 1% and is considered PD-L1 positive (and thus the subjectis eligible for anti-PD therapy).

Examples of Images for Interpretation of PD-L1 IHC 22C3 pharmDx Staining

FIGS. 5 through 18 provide examples of images of tissue sections stainedwith the PD-L1 IHC 22C3 pharmDx kit.

FIG. 5 provides an image of a stained tissue section showing differentintensities of PD-L1 on tumor cells.

FIG. 6 provides an image of a stained tissue section showing PD-L1positive inflammatory cells.

FIG. 7 provides an image of a stained tissue section showing cytoplasmicand membrane staining. Labeled arrows show complete staining, partialstaining, cytoplasmic staining, and membrane staining.

FIG. 8 provides an image of a stained tissue section showing anedge-staining artifact (example of artifact indicated by arrow).

FIG. 9 provides an image of a stained tissue section showing acytoplasmic blush artifact (example of artifact indicated by arrow).

FIG. 10 provides an image of a stained tissue section showing theartifact of staining of necrotic tissue (examples of artifact indicatedby arrows).

FIG. 11 provides an image of a stained tissue section showing an exampleof HNSCC with a CPS of 0%. Examples of negative MIC and tumor cells areindicted with arrows.

FIG. 12 provides an image of a stained tissue section showing Example ofHNSCC with a CPS of 1%. Examples of negative and positive MICs and tumorcells are indicated with arrows.

FIG. 13 provides an image of a stained tissue section showing Example ofHNSCC with a CPS of 55%. Examples of negative and positive MICs andtumor cells are indicated with arrows.

FIG. 14 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 0%. Examples of negative MIC and tumorcells are indicted with arrows.

FIG. 15 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 1%. Examples of negative and positiveMICs and negative tumor cells are indicted with arrows.

FIG. 16 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 10%. Examples of negative and positiveMICs and tumor cells are indicated with arrows.

FIG. 17 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 40%. Examples of negative and positiveMICs and tumor cells are indicated with arrows.

FIG. 18 provides an image of a stained tissue section showing Example ofGastric Carcinoma with a CPS of 100%. Example of positive tumor cell isindicated with an arrow.

Kits

Also provided by this disclosure are kits that provide reagents foranalyzing a tissue section(s) for determining the eligibility of asubject having a malignancy for treatment with an anti-PD therapeuticagent according to the methods described herein.

For example, a kit may contain a detectable PD-L1 specific binding agentand instructions for determining and/or calculating a combined positivescore (CPS). The instructions can thus include descriptions for sampleanalysis, for interpreting the results of the test, and/or forcalculating a CPS score to determine the eligibility of a subject havinga malignancy for treatment with an anti-PD therapeutic agent, e.g., ananti-PD-L1 antibody therapy. Such instructions for practicing thesubject methods and interpreting the results are generally recorded on asuitable recording medium. For example, the instructions may be printedon a substrate, such as paper or plastic, etc. As such, the instructionsmay be present in the kits as a package insert, in the labeling of thecontainer of the kit or components thereof (i.e., associated with thepackaging or subpackaging), etc. In other embodiments, the instructionsare present as an electronic storage data file present on a suitablecomputer readable storage medium, e.g., CD-ROM, diskette, USB drive,Cloud storage location, etc. In yet other embodiments, the actualinstructions are not present in the kit, but means for obtaining theinstructions from a remote source, e.g., via the internet, are provided.An example of this embodiment is a kit that includes a web address wherethe instructions can be viewed and/or from which the instructions can bedownloaded. As with the instructions, this means for obtaining theinstructions is recorded on a suitable substrate.

The kit can further include any one or more of the following: a positivecontrol sample, a negative control sample, a detectable binding agentfor a marker specific for mononuclear inflammatory cells (MIC), e.g.,CD3, CD5, CD4, CD7, CD8, CD20, and other markers of MIC, one or morereagents for performing an immunohistochemistry (IHC) staining reactionon a tumor tissue sample from a subject.

The various components of the kit may be present in separate containersor certain compatible components may be pre-combined into a singlecontainer, as desired.

Examples Example 1

The main challenge around interpretation of tumor tissue stains forPD-L1 (e.g., TPS and MIDS scores, described in detail below) is todistinguish tumor from immune cells. This is especially true in gastriccarcinoma since tumor and immune cells are of similar size and thereforevery challenging to differentiate. Importantly, recent studies indicatethat in certain tumor types expression of PD-L1 in immune as well as intumor cells may be a good predictor of efficacy of anti-PD-1immunotherapy (e.g., like pembrolizumab).

To address the challenges around companion diagnostic assay developmenttimelines and scoring interpretation, we propose below a CombinedPositive Score (CPS).

CPS for Use in Gastric Carcinoma

Samples Analyzed

Specimens from subjects having gastric carcinoma patients are analyzed.These samples can be from patients prior to treatment, during treatment,or after an initial round of treatment with a therapeutic agent, e.g.,pembrolizumab.

Tissue Specimen Preparation and Staining

Specimens for analysis are formalin-fixed and paraffin-embedded (FFPE)tissue sections. Sections are cut to a desired thickness (e.g., 4 umthickness), placed on charged slides, and dried in an oven for one hour.For example, human tissue sections can be dried at 56-60° C. The cutsections can be stored in the dark at 2-8° C. and stained with the PD-L1IHC assay within 6 months.

The IHC staining for PD-L1 expression is performed using the DakoAutostainer Link 48 platform (Dako AS480) and an automated stainingprotocol validated for the PD-L1 IHC 22C3 pharmDx assay.Deparaffinization, rehydration and target retrieval of the tissuesections is performed in the PT Link (Dako PT100) using a 3-in-1procedure. Following incubation with the monoclonal mouse anti-humanPD-L1 antibody (clone 22C3) or the Negative Control Reagent (NCR) (mouseIgG isotype control), specimens are incubated with anti-mouse linkerantibody specific to the host species of the primary antibody, and thenincubated with a ready-to-use visualization reagent consisting ofsecondary antibody molecules and horseradish peroxidase moleculescoupled to a dextran polymer backbone. The enzymatic conversion of thesubsequently added 3,3′-diaminobenzidine tetrahydrochloride (DAB)chromogen followed by DAB enhancer results in precipitation of a visiblereaction product at the site of antigen. The specimens are thencounterstained with Hematoxylin and coverslipped. Results areinterpreted by direct observation using a light microscope. Assayperformance is optimized for sensitivity with minimum non-specificstaining by adjusting primary antibody concentration and reagentincubation times.

Staining Interpretation

Hematoxylin and Eosin stain (H&E) is used by the pathologist to confirmdiagnosis and situate the tumor. Hematoxylin counterstain on the PD-L1slide is used to estimate the number of cells. Tumor cells are typicallylarger than mononuclear inflammatory cells. Initially, PD-L1 expressionis determined and interpreted as follows:

1. The Tumor Proportion Score (TPS): the percentage of tumor cellsexpressing PD-L1 on the cell membrane. Linear partial or complete cellmembrane staining is interpreted as positive for PD-L1.

2. Mononuclear Inflammatory Density Score (MIDS): the ratio of thenumber of PD-L1 expressing mononuclear inflammatory cells infiltratingor adjacent to the tumor compared to the total number of tumor cells.The MIDS is recorded at a scale from 0 to 4 with (0=None; 1=Present, butless than one MIC for every 100 tumor cells (<1%; a negative result);2=At least one MIC for every 100 tumor cells, but less than one MIC per10 tumor cells (1-9%; a positive result); 3=At least one MIC for every10 tumor cells, but fewer MIC's than tumor cells (10-99%; a positiveresult); 4=At least as many MIC's as tumor cells (≥100%; a positiveresult).

3. Combined Positive Score (CPS): the ratio of the number of PD-L1positive tumor cells and PD-L1 positive mononuclear inflammatory cells(MIC) within the tumor nests and the adjacent supporting stroma(numerator) compared to the total number tumor cells (denominator; i.e.,the number of PD-L1 positive and PD-L1 negative tumor cells). (Seedetailed description above for further details.) PD-L1 expression at anyintensity is considered positive, i.e., weak (1+), moderate (2+), orstrong (3+).

A cut-off is the score that differentiates diagnostically positive fromdiagnostically negative. The cut-off can be set to achieve the followinggoals:

1. Identify all responders (i.e., no false negatives); and 2. Minimizethe number of non-responders (i.e., false positives).

It is expected that setting the cut-off at ≥1% for a positive result forthe scores above, CPS will identify subjects who are responsive toanti-PD therapy that are missed by the TPS and MIDS analyses describedabove. The CPS scoring method is very reproducible between pathologistsand therefore an excellent scoring algorithm to interpret PD-L1expression to identify subjects eligible for anti-PD therapy.

CPS Used in Other Cancers

The CPS approach is generally applicable to any cancers expressing PD-L1in either tumor and/or immune cells. For example, CPS can be used toanalyze triple negative breast carcinoma using a similar cut-off valueas described above.

Exemplary Embodiments

Non-limiting examples of embodiments of certain aspects of the subjectdisclosure are provided below.

1. A method for determining the eligibility of a subject having amalignancy for treatment with an anti-PD therapeutic agent, the methodcomprising: determining the number of viable PD-L1 positive tumor cells,the number of viable PD-L1 negative tumor cells, and the number ofviable PD-L1 positive mononuclear inflammatory cells (MIC) in a tumortissue sample from a subject having a malignancy; calculating a combinedpositive score (CPS) for the tumor tissue sample using the formula:

${CPS} = {\frac{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{positive}{MIC}}}{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{negative}{tumor}{cells}}} \times 100\%}$

wherein the subject is eligible for treatment with an anti-PDtherapeutic agent when the CPS is above a threshold.

2. The method of embodiment 1, wherein the threshold is from about 10%to about 1%.

3. The method of embodiment 1 or 2, wherein the threshold is 1%.

4. The method of any one of embodiments 1 to 3, wherein the tumor tissuesample is a tissue section of a tumor biopsy.

5. The method of embodiment 4, wherein PD-L1 is detected byimmunohistochemistry (IHC) staining.

6. The method of embodiment 4 or 5, wherein the tumor tissue section isa formalin fixed and embedded in paraffin wax (FFPE) tumor tissuesection.

7. The method of any one of embodiments 4 to 6, wherein the tissuesection is stained.

8. The method of embodiment 7, wherein the stain is a hematoxylin andeosin (H&E) stain.

9. The method of any one of embodiments 4 to 8, wherein the viable PD-L1positive tumor cells, the number of viable PD-L1 negative tumor cells,and the number of viable PD-L1 positive MIC are counted in the tumornests and the adjacent supporting stroma of the tumor tissue sample.

10. The method of any one of embodiments 1 to 3, wherein the tumortissue sample is a cell suspension.

11. The method of embodiment 10, wherein the number of viable PD-L1positive tumor cells, the number of viable PD-L1 negative tumor cells,and the number of viable PD-L1 positive MIC in the tumor tissue sampleare determining by flow cytometry.

12. The method of any one of embodiments 1 to 11, wherein one or moreadditional marker is detected in the tumor tissue sample.

13. The method of embodiment 12, wherein the marker is specific for MIC.

14. The method of embodiment 13, wherein the marker is selected from thegroup consisting of: CD3, CD5, CD4, CD7, CD8, and CD20.

15. The method of any one of embodiments 12 to 14, wherein PD-L1 and theone or more additional marker are detected simultaneously.

16. The method of any one of embodiments 12 to 14, wherein PD-L1 and theone or more additional marker are detected sequentially.

17. The method of any one of embodiments 1 to 16, wherein the methodfurther comprises, prior to the determining step, contacting the tumortissue sample with a detectable anti-PD-L1 binding agent.

18. The method of embodiment 17, wherein the detectable anti-PD-L1binding agent comprises an anti-PD-L1 antibody or binding fragmentthereof.

19. The method of any one of embodiments 1 to 3, wherein the number ofviable PD-L1 positive tumor cells, the number of viable PD-L1 negativetumor cells, and the number of viable PD-L1 positive MIC in the tumortissue sample are determined by single cell sequencing.

20. The method of any preceding embodiment, wherein the malignancy isselected from the group consisting of: gastric cancer, head and neckcancer, renal cell carcinoma, urothelial/bladder carcinoma, ovariancarcinoma, myeloma, melanoma, lung cancer, squamous cell carcinoma,classical Hodgkin's lymphoma, and breast cancer (e.g., triple negativebreast cancer, hormone receptor positive (ER and/or PR) and Her2positive breast cancer), small cell lung cancer, salivary glandcarcinoma, vulvar carcinoma, thyroid carcinoma, anal canal carcinoma,biliary carcinoma, mesothelioma, cervical carcinoma, and neuroendocrinecarcinoma.

21. The method of embodiment 18, wherein the malignancy is gastriccancer.

22. The method of embodiment 18, wherein the malignancy is head and neckcancer.

23. The method of embodiment 18, wherein the head and neck cancer ishead and neck squamous cell carcinoma (HNSCC).

24. The method of any preceding embodiment, wherein the anti-PDtherapeutic agent inhibits the anti-cell death activity of PD-1/PD-L1.

25. The method of any preceding embodiment, wherein the anti-PDtherapeutic agent comprises an anti-PD or anti-PD-L1 specific antibodyor binding fragment thereof.

26. The method of embodiment 25, wherein the anti-PD therapeutic agentis selected from the group consisting of: Avelumab (MSB0010178C),Nivolumab, Pembrolizumab, BMS-936559, MPDL3280A, Pidilizumab, andMEDI4736.

27. The method of embodiment 23, wherein the anti-PD therapeutic agentis Avelumab.

28. The method of any preceding embodiment, wherein the subject is ahuman.

29. A kit for determining the eligibility of a subject having amalignancy for treatment with an anti-PD therapeutic agent, comprising:a detectable PD-L1 specific binding agent; and instructions forcalculating a combined positive score (CPS).

30. The kit of embodiment 29, further comprising a positive and negativecontrol sample.

31. The kit of embodiment 29 or 30, further comprising a detectablebinding agent for a marker specific for mononuclear inflammatory cells(MIC).

32. The kit of embodiment 31, wherein the marker specific for MIC isselected from the group consisting of: CD3, CD5, CD4, CD7, CD8, andCD20.

33. The kit of any one of embodiments 29 to 32, further comprising oneor more reagents for performing an immunohistochemistry (IHC) stainingreaction on a tumor tissue sample from a subject.

A method of treatment is provided. In some embodiments, the methodcomprises:

determining the number of viable PD-L1 positive tumor cells, the numberof viable PD-L1 negative tumor cells, and the number of viable PD-L1positive mononuclear inflammatory cells (MIC) in a tumor tissue samplefrom a subject having a malignancy; calculating a combined positivescore (CPS) for the tumor tissue sample using the formula:

${CPS} = {\frac{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{positive}{MIC}}}{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{negative}{tumor}{cells}}} \times 100\%}$

and treating the subject with an anti-PD therapeutic agent if the CPS isabove a threshold.

It will also be recognized by those skilled in the art that, while theinvention has been described above in terms of preferred embodiments, itis not limited thereto. Various features and aspects of the abovedescribed invention may be used individually or jointly. Further,although the invention has been described in the context of itsimplementation in a particular environment, and for particularapplications those skilled in the art will recognize that its usefulnessis not limited thereto and that the present invention can bebeneficially utilized in any number of environments and implementations.Accordingly, the claims set forth below should be construed in view ofthe full breadth and spirit of the invention as disclosed herein.

What is claimed is:
 1. A method for determining the eligibility of asubject having a malignancy for treatment with an anti-PD therapeuticagent, the method comprising: determining the number of viable PD-L1positive tumor cells, the number of viable PD-L1 negative tumor cells,and the number of viable PD-L1 positive mononuclear inflammatory cells(MIC) in a tumor tissue sample from a subject having a malignancy;calculating a combined positive score (CPS) for the tumor tissue sampleusing the formula:${CPS} = {\frac{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{positive}{MIC}}}{{{PD} - L1{positive}{tumor}{cells}} + {{PD} - L1{negative}{tumor}{cells}}} \times 100\%}$wherein the subject is eligible for treatment with an anti-PDtherapeutic agent when the CPS is above a threshold.
 2. The method ofclaim 1, wherein the threshold is from about 10% to about 1%.
 3. Themethod of claim 1, wherein the threshold is 1%.
 4. The method of claim1, wherein the tumor tissue sample is a tissue section of a tumorbiopsy.
 5. The method of claim 4, wherein PD-L1 is detected byimmunohistochemistry (IHC) staining.
 6. The method of claim 4, whereinthe tumor tissue section is a formalin fixed and embedded in paraffinwax (FFPE) tumor tissue section.
 7. The method of claim 4, wherein thetissue section is stained.
 8. The method of claim 7, wherein the stainis a hematoxylin and eosin (H&E) stain.
 9. The method of claim 4,wherein the viable PD-L1 positive tumor cells, the number of viablePD-L1 negative tumor cells, and the number of viable PD-L1 positive MICare counted in the tumor nests and the adjacent supporting stroma of thetumor tissue sample.
 10. The method of claim 1, wherein the tumor tissuesample is a cell suspension.
 11. The method of claim 10, wherein thenumber of viable PD-L1 positive tumor cells, the number of viable PD-L1negative tumor cells, and the number of viable PD-L1 positive MIC in thetumor tissue sample are determining by flow cytometry.
 12. The method ofclaim 1, wherein one or more additional marker is detected in the tumortissue sample.
 13. The method of claim 12, wherein the marker isspecific for MIC or is selected from the group consisting of: CD3, CD5,CD4, CD7, CD8, and CD20.
 14. The method of claim 1, wherein the methodfurther comprises, prior to the determining step, contacting the tumortissue sample with an anti-PD-L1 antibody or binding fragment thereof.15. The method of claim 1, wherein the number of viable PD-L1 positivetumor cells, the number of viable PD-L1 negative tumor cells, and thenumber of viable PD-L1 positive MIC in the tumor tissue sample aredetermined by single cell sequencing.
 16. The method of claim 1, whereinthe malignancy is selected from the group consisting of: gastric cancer,head and neck cancer, renal cell carcinoma, urothelial/bladdercarcinoma, ovarian carcinoma, myeloma, melanoma, lung cancer, squamouscell carcinoma, classical Hodgkin's lymphoma, and breast cancer (e.g.,triple negative breast cancer, hormone receptor positive (ER and/or PR)and Her2 positive breast cancer), small cell lung cancer, salivary glandcarcinoma, vulvar carcinoma, thyroid carcinoma, anal canal carcinoma,biliary carcinoma, mesothelioma, cervical carcinoma, and neuroendocrinecarcinoma.
 17. The method of claim 1, wherein the anti-PD therapeuticagent inhibits the anti-cell death activity of PD-1/PD-L1.
 18. Themethod of claim 1, wherein the anti-PD therapeutic agent comprises ananti-PD or anti-PD-L1 specific antibody or binding fragment thereof. 19.The method of claim 1, wherein the anti-PD therapeutic agent is selectedfrom the group consisting of: Avelumab (MSB0010178C), Nivolumab,Pembrolizumab, BMS-936559, MPDL3280A, Pidilizumab, and MEDI4736.
 20. Akit for determining the eligibility of a subject having a malignancy fortreatment with an anti-PD therapeutic agent, comprising: a detectablePD-L1 specific binding agent; and instructions for calculating acombined positive score (CPS).